23andMe and Illumina Forge Consumer Genomics Goliath

23andMe, the personal genomics start-up with Google connections, and high-flying genomic analysis company Illumina have struck a bellwether deal in the fledgling field of consumer genotyping.

Although neither company has issued an official statement on the deal, Illumina CEO Jay Flatley said he was “extremely excited” about the partnership with 23andMe during a Q2 earnings teleconference last month. He also elaborated on the emerging field of consumer genomics in remarks at an investors’ conference in New York earlier in August.

23andMe (see First Base, Bio-IT World, June 2007) was co-founded last year by Anne Wojcicki (wife of Google co-founder Sergey Brin) and Linda Avey, a former business development executive with Affymetrix and Perlegen. The company has received Series A funding from Google and Genentech, among others. The firm’s mission is to allow consumers to obtain “broad, secure, and private access to trustworthy and accurate individual genetic information” as well as offering “educational and scientific resources with which to interpret and understand” individual genome sequences.

Exciting Market“In addition to [our] traditional research and pharma customers, we believe that consumer genotyping will ultimately be the largest market,” Flatley told analysts during Illumina’s second-quarter earnings call last month. “We have developed a collaboration with 23andMe to provided genotyping services for the consumer-based market.”

Flatley reiterated his excitement about the nascent field of consumer genomics in remarks at the Leerink Swann Life Sciences Tools conference in New York a couple of weeks later. Said Flatley: “We see this as a very exciting market in the next couple of years… A few years ago, investors would always ask, ‘Is the whole-genome market a flash in the pan? Is it going to be over in a year?’ And we always said, ‘No.’ The market for genotyping is everybody! More than ever we believe that.”

In a veiled reference to 23andMe, Flatley said, “Very shortly you will have commercial organizations supporting the notion of doing consumer genotyping. We think the uptake of this will be very interesting to watch.”

Flatley added: “Our current feeling is that, most likely, consumer genotyping would be done as a service. We don’t think there are going to be people doing this in their garages to genotype their family! We really think this will be a service-oriented business. Samples will come to Illumina or other service providers, and the genotyping will be done centrally.”

The precise nature of 23andMe’s debut commercial offering will become clear in the next few months. A handful of consumer genomics companies currently offer direct-to-consumer gene tests. For example, DNA Direct offers a handful of disease-related gene tests in the $200-$500 range, as well as an Ashkenazi Jewish carrier test for $1266. Sciona’s MyCellf genotype analysis of 19 genes costs under $300. IBM’s popular Genographic Project kit, which allows individuals to trace a portion of their genealogical history, costs $99.

Illumina offers a new chip with one million single-nucleotide polymorphisms (SNPs), which costs around $600 depending on volume. Its best-selling bead array is the HumanHap550, which analyzes 550,000 tag SNPs from the International HapMap project and costs $300-$450.

SNPs to SequenceSpeaking in general terms, Flatley said that if organizations were looking to screen medically relevant SNPs, they could “troll through the literature to discover every SNP with a [disease] association.” Illumina’s new iSelect product line allows customers to add custom SNPs to the company’s bead arrays. “We can take a [HumanCNV370-Duo chip] and augment it with an additional 60,000 SNPs you’ve gleaned from the literature…or you can do that on the [HumanHap] 550 chip as well. It allows customers to put in a custom set [of SNPs] as well as the SNPs that come on the chip,” Flatley said.

One of the intriguing aspects of 23andMe’s partnership with Illumina is the potential ease of transition from genotyping to full-blown sequencing, once the cost of sequencing drops into the neighborhood of the much-touted “$1000 genome.” Last year, Illumina acquired Solexa, the second company to commercially release a next-generation sequencing platform. The Illumina Genome Analyzer is fast gaining critical and commercial momentum – the number of scientific papers is growing rapidly (see, for example, Next-Generation Sequencing Invades Microarray Turf, at Bio-IT World.com), and sales are beating forecasts. Flatley announced last month that one unspecified customer had just ordered 20 sequencing instruments.

Asked about the current cost of human genome sequencing, Flatley said, “We’re not quite at $100,000, but getting awfully close. We expect to be there by year end.” Unclear for now is the degree to which a complete human genome sequence analysis would augment the medical and health information that could be extracted from a comprehensive panel of 500,000 or one million SNPs.